Research workbench
3,4-dihydroxy-2-butanone 4-phosphate synthase from methanococcus jannaschii
Analyse 3,4-dihydroxy-2-butanone 4-phosphate synthase from methanococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SNN
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,4-dihydroxy-2-butanone 4-phosphate synthase
- EC
- 5.4.99.-
- UniProt
- Q60364
- Ligands
- 5RP, CA, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 5.4.99.-) | protein | 219 | 45% helix, 22% strand | Q60364 |
| B | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 5.4.99.-) | protein | 219 | 46% helix, 22% strand | Q60364 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.97 | 31 | 5RP, ZN, CA |
| 2 | 258 | 0.78 | 0.91 | 37 | 5RP, ZN, CA |
| 3 | 121 | 0.78 | 0.96 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2590 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 1SNN · 3,4-dihydroxy-2-buta 4-phosphate synthase from Methanococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q60364 · AlphaFold monomer V2.0 prediction for 3,4-dihydroxy-2-butanone 4-phosphate synthase… · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q60364
- Elsewhere: RCSB PDB 1SNN · PDBe 1SNN · UniProt Q60364
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